DOCSLIB.ORG

Genomic Approaches to Dissect Innate Immune Pathways

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genomic Approaches to Dissect Innate Immune Pathways Genomic Approaches to Dissect Innate Immune Pathways The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Lee, Mark N. 2012. Genomic Approaches to Dissect Innate Immune Pathways. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10403683 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA © 2012 – Mark N. Lee All rights reserved Dissertation Advisor: Dr. Nir Hacohen Mark N. Lee Genomic approaches to dissect innate immune pathways Abstract The innate immune system is of central importance to the early containment of infection. When receptors of innate immunity recognize molecular patterns on pathogens, they initiate an immediate immune response by inducing the expression of cytokines and other host defense genes. Altered expression or function of the receptors, the molecules that mediate the signal transduction cascade, or the cytokines themselves can predispose individuals to infectious or autoimmune diseases. Here we used genomic approaches to uncover novel components underlying the innate immune response to cytosolic DNA and to characterize variation in the innate immune responses of human dendritic cells to bacterial and viral ligands. In order to identify novel genes involved in the cytosolic DNA sensing pathway, we first identified candidate proteins that interact with known signaling molecules or with dsDNA in the cytoplasm. We then knocked down 809 proteomic, genomic, or domain-based candidates in a high-throughput siRNA screen and measured cytokine production after DNA stimulation. We identified ABCF1 as a critical protein that associates with DNA and the known DNA-sensing components, HMGB2 and IFI16. We also found that CDC37 regulates stability of the signaling molecule, TBK1, and that chemical inhibition of CDC37 as well as of several other pathway regulators (HSP90, PPP6C, PTPN1, and TBK1) potently modulates the innate immune response to DNA and to retroviral infection. These proteins represent potential therapeutics targets for infectious and autoimmune diseases that are associated with the cytosolic DNA response. iii We also developed a high-throughput functional assay to assess variation in responses of human monocyte-derived dendritic cells to LPS (receptor: TLR4) or influenza (receptors: RIG-I and TLR3), with the goal to ultimately map genetic variants that influence expression levels of pathogen-responsive genes. We compared the variation in expression between the dendritic cells of 30 different individuals, and within paired samples from 9 of these individuals collected several months later. We found genes that have significant inter- vs. intra-individual variation in response to the stimuli, suggesting that there is a substantial genetic component underlying variation in these responses. Such variants may help to explain differences between individuals’ risk for infectious, autoimmune, or other inflammatory diseases. iv TABLE OF CONTENTS TITLE PAGE .......................................................................................................................... I COPYRIGHT PAGE ............................................................................................................ II ABSTRACT ......................................................................................................................... III TABLE OF CONTENTS ...................................................................................................... V LIST OF TABLES AND FIGURES ................................................................................. VII ACKNOWLEDGMENTS ................................................................................................ VIII INTRODUCTION .................................................................................................................. 1 The detection of pathogens by the innate immune system .......................................................... 1 Toll-like receptors (TLRs) ........................................................................................................... 2 RIG-like receptors (RLRs) .......................................................................................................... 3 Cytosolic DNA sensors ............................................................................................................... 4 Signal transduction cascades in the innate immune system ........................................................ 8 The role of the innate immune system in host defense .............................................................. 11 Dysregulation of the innate immune system can lead to autoimmune/autoinflammatory disease ....................................................................................................................................... 16 Characterization of variation in the human innate immune system .......................................... 22 Overview of objectives .............................................................................................................. 25 CHAPTER 1: AN INTEGRATIVE APPROACH IDENTIFIES CRITICAL REGULATORS OF THE INNATE IMMUNE RESPONSE TO CYTOSOLIC DNA AND RETROVIRAL INFECTION ................................................................................... 26 Author Contributions and Acknowledgements ....................................................................... 27 Abstract ....................................................................................................................................... 29 Introduction ................................................................................................................................ 30 Results .......................................................................................................................................... 33 Generation of a candidate gene set by curation and quantitative proteomics ........................... 33 High-throughput loss-of-function screening of candidates and network analysis .................... 36 Validation by targeted knockout, cDNA rescue, and chemical inhibition ................................ 36 Quantitative proteomics analysis of the DNA-sensing network ............................................... 42 v Innate immune response to retroviral infection in TREX1 mutant cells .................................... 45 Discussion .................................................................................................................................... 48 Materials and Methods .............................................................................................................. 50 CHAPTER 2: A GENETICAL GENOMICS APPROACH TO UNDERSTANDING THE REGULATORY MECHANISMS OF HOST-PATHOGEN INTERACTIONS IN HUMANS............................................................................................................................... 58 Author Contributions and Acknowledgements ....................................................................... 59 Abstract ....................................................................................................................................... 61 Introduction ................................................................................................................................ 62 Results ......................................................................................................................................... 65 Establishment of a system to quantitatively measure innate immune responses in MoDCs .... 65 Comparison of LPS- and influenza-stimulated gene expression in 30 donors .......................... 67 Comparison of LPS- and influenza-stimulated gene expression within 9 serial replicates ...... 70 Selection of reporter genes ........................................................................................................ 71 Comparison of LPS-, influenza-, and IFNβ-stimulated gene expression in 133 donors ........... 73 Discussion .................................................................................................................................... 75 Materials and Methods .............................................................................................................. 77 CONCLUSION ..................................................................................................................... 81 REFERENCES ..................................................................................................................... 87 Appendix A: Supporting information for Chapter 1 ............................................................ 106 Appendix B: Supporting information for Chapter 2 ............................................................ 123 vi LIST OF TABLES AND FIGURES Tables Supplementary Table 1.1. STING-interacting SILAC hits ........................................................ 112 Supplementary Table 1.2. DNA-interacting SILAC hits ........................................................... 113 Supplementary Table 1.3a. siRNA screen (DNA SILAC) ......................................................... 114 Supplementary Table 1.3b. siRNA screen (Microarray) ............................................................ 115 Supplementary Table
Load more

Recommended publications
  • ABCG1 (ABC8), the Human Homolog of the Drosophila White Gene, Is a Regulator of Macrophage Cholesterol and Phospholipid Transport
    ABCG1 (ABC8), the human homolog of the Drosophila white gene, is a regulator of macrophage cholesterol and phospholipid transport Jochen Klucken*, Christa Bu¨ chler*, Evelyn Orso´ *, Wolfgang E. Kaminski*, Mustafa Porsch-Ozcu¨ ¨ ru¨ mez*, Gerhard Liebisch*, Michael Kapinsky*, Wendy Diederich*, Wolfgang Drobnik*, Michael Dean†, Rando Allikmets‡, and Gerd Schmitz*§ *Institute for Clinical Chemistry and Laboratory Medicine, University of Regensburg, 93042 Regensburg, Germany; †National Cancer Institute, Laboratory of Genomic Diversity, Frederick, MD 21702-1201; and ‡Departments of Ophthalmology and Pathology, Columbia University, Eye Research Addition, New York, NY 10032 Edited by Jan L. Breslow, The Rockefeller University, New York, NY, and approved November 3, 1999 (received for review June 14, 1999) Excessive uptake of atherogenic lipoproteins such as modified low- lesterol transport. Although several effector molecules have been density lipoprotein complexes by vascular macrophages leads to proposed to participate in macrophage cholesterol efflux (6, 9), foam cell formation, a critical step in atherogenesis. Cholesterol efflux including endogenous apolipoprotein E (10) and the cholesteryl mediated by high-density lipoproteins (HDL) constitutes a protective ester transfer protein (11), the detailed molecular mechanisms mechanism against macrophage lipid overloading. The molecular underlying cholesterol export in these cells have not yet been mechanisms underlying this reverse cholesterol transport process are characterized. currently not fully understood. To identify effector proteins that are Recently, mutations of the ATP-binding cassette (ABC) trans- involved in macrophage lipid uptake and release, we searched for porter ABCA1 gene have been causatively linked to familial HDL genes that are regulated during lipid influx and efflux in human deficiency and Tangier disease (12–14).
    [Show full text]
  • A Comprehensive Mapping of the Structure and Gene Organisation in the Sheep MHC Class I Region N
    Siva Subramaniam et al. BMC Genomics (2015) 16:810 DOI 10.1186/s12864-015-1992-4 RESEARCH ARTICLE Open Access A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region N. Siva Subramaniam1, EF Morgan1, JD Wetherall1, MJ Stear2,3* and DM Groth1 Abstract Background: The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods: CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results: Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms.
    [Show full text]
  • Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
    Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice.
    [Show full text]
  • Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response
    International Journal of Molecular Sciences Article Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response Viktor Hlaváˇc 1,2 , Radka Václavíková 1,2, Veronika Brynychová 1,2, Renata Koževnikovová 3, Katerina Kopeˇcková 4, David Vrána 5 , Jiˇrí Gatˇek 6 and Pavel Souˇcek 1,2,* 1 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; [email protected] (V.H.); [email protected] (R.V.); [email protected] (V.B.) 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic 3 Department of Oncosurgery, Medicon Services, 140 00 Prague, Czech Republic; [email protected] 4 Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, 150 06 Prague, Czech Republic; [email protected] 5 Department of Oncology, Medical School and Teaching Hospital, Palacky University, 779 00 Olomouc, Czech Republic; [email protected] 6 Department of Surgery, EUC Hospital and University of Tomas Bata in Zlin, 760 01 Zlin, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-267-082-711 Received: 19 November 2020; Accepted: 11 December 2020; Published: 15 December 2020 Abstract: Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105).
    [Show full text]
  • It Is Illeg Al to P O St Th Is Co P Yrig H Ted P D F O N an Y W Eb Site. It Is Illegal
    Letters to the Editor It is Geneillegal Expression to Profiling post ofthis the xMHC copyrighted Region and HIST1H4C PDF encodeon histones.any Strong website. evidence of associations Reveals 9 Candidate Genes in Schizophrenia was observed within and around histone genes in schizophrenia.2 Abnormal expression of genes related to nucleosome and histone To the Editor: Strong association of the extended major structure and function has also been found in both schizophrenia 3 histocompatibility complex (xMHC) region on human patients and their siblings. MRPS18B encodes ribosomal protein chromosome 6 with schizophrenia has been supported by a that helps in mitochondrial protein synthesis. TUBB encodes number of genome-wide association studies.1 However, since tubulin that is the major constituent of microtubules. Altered the xMHC region is featured by numerous polymorphisms, expression of TUBB has been reported in a previous microarray 4 dense gene clusters, and strong linkage disequilibrium, it is study in schizophrenia patients. ABCF1 and BTN3A3 are difficult to attribute the association to specific genes. A targeted immune-related genes. BTN3A3 is involved in T-cell activity scrutinization of gene expression in the xMHC region can in adaptive immune response. ABCF1 enhances protein provide valuable candidate genes for future validation. Here synthesis and promotes inflammation. Decreased expression we utilize 2 real-time polymerase chain reaction (PCR)–based of ABCF1 had been found in the whole blood of patients with platforms and 2 sample sets to investigate protein-coding gene schizophrenia and identified as a hub gene in a gene expressional 5 expressions in the xMHC region in peripheral blood leukocytes subnetwork.
    [Show full text]
  • RNA-Seq Reveals Conservation of Function Among the Yolk Sacs Of
    RNA-seq reveals conservation of function among the PNAS PLUS yolk sacs of human, mouse, and chicken Tereza Cindrova-Daviesa, Eric Jauniauxb, Michael G. Elliota,c, Sungsam Gongd,e, Graham J. Burtona,1, and D. Stephen Charnock-Jonesa,d,e,1,2 aCentre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, United Kingdom; bElizabeth Garret Anderson Institute for Women’s Health, Faculty of Population Health Sciences, University College London, London, WC1E 6BT, United Kingdom; cSt. John’s College, University of Cambridge, Cambridge, CB2 1TP, United Kingdom; dDepartment of Obstetrics and Gynaecology, University of Cambridge, Cambridge, CB2 0SW, United Kingdom; and eNational Institute for Health Research, Cambridge Comprehensive Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom Edited by R. Michael Roberts, University of Missouri-Columbia, Columbia, MO, and approved May 5, 2017 (received for review February 14, 2017) The yolk sac is phylogenetically the oldest of the extraembryonic yolk sac plays a critical role during organogenesis (3–5, 8–10), membranes. The human embryo retains a yolk sac, which goes there are limited data to support this claim. Obtaining experi- through primary and secondary phases of development, but its mental data for the human is impossible for ethical reasons, and importance is controversial. Although it is known to synthesize thus we adopted an alternative strategy. Here, we report RNA proteins, its transport functions are widely considered vestigial. sequencing (RNA-seq) data derived from human and murine yolk Here, we report RNA-sequencing (RNA-seq) data for the human sacs and compare them with published data from the yolk sac of and murine yolk sacs and compare those data with data for the the chicken.
    [Show full text]
  • The ATP-Binding Cassette Transporter ABCF1 Is a Hepatic Oncofetal
    Cancer Letters 457 (2019) 98–109 Contents lists available at ScienceDirect Cancer Letters journal homepage: www.elsevier.com/locate/canlet Original Articles The ATP-binding cassette transporter ABCF1 is a hepatic oncofetal protein T that promotes chemoresistance, EMT and cancer stemness in hepatocellular carcinoma Sze Wai Funga,b,c, Phyllis Fung-Yi Cheunga,d,e, Chi Wai Yipa,c,f, Linda Wing-Chi Nga, Tan To Cheungc, Charing Ching-Ning Chonga, Carol Leea, Paul Bo-San Laia, Anthony Wing-Hung Chang, George Sai-Wah Tsaob, Chi-Hang Wongh, Stephen Lam Chanh, ∗ Kwok Wai Log, Siu Tim Cheunga,i, a Department of Surgery, The Chinese University of Hong Kong, Hong Kong b School of Biomedical Sciences, The University of Hong Kong, Hong Kong c Department of Surgery, The University of Hong Kong, Hong Kong d Division of Solid Tumor Translational Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany e German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany f RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan g Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong h Department of Clinical Oncology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong i Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong ARTICLE INFO ABSTRACT Keywords: ATP-binding cassette (ABC) transporters mediate multidrug resistance and cancer stem cell properties in various HCC model systems. Yet, their biological significance in cancers, especially in hepatocellular carcinoma (HCC), re- Multidrug resistance mains unclear.
    [Show full text]
  • Genetics of Abca4-Associated Diseases and Retinitis Pigmentosa
    GENETICS OF ABCA4-ASSOCIATED DISEASES AND RETINITIS PIGMENTOSA Yajing (Angela) Xie Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2016 © 2016 Yajing (Angela) Xie All rights reserved ABSTRACT Genetics of ABCA4-Associated Diseases and Retinitis Pigmentosa Yajing (Angela) Xie Inherited retinal dystrophies encompass a broad group of genetic disorders affecting visual functions in as high as 1 in 3,000 individuals around the world. Common symptoms include loss of central, periphery, or night visions, and in severe cases progression to complete blindness. Syndromic forms also exist involving abnormalities in other parts of the body. Currently, more than 250 genes representing a wide variety of functional roles have been shown to be responsible for the disease phenotypes. Moreover, mutations in the same gene sometimes cause different phenotypes while mutations in multiple genes can give rise to the same clinical subtype, further demonstrating the level of complexity in these disorders. Such genetic heterogeneity has substantially complicated the process of pinpointing precise genetic causes underlying these conditions. The goal of my thesis research is to clarify the genetic causes underlying retinal dystrophies, with a primary focus on phenotypes resembling ABCA4-associated diseases and retinitis pigmentosa in both syndromic and non-syndromic forms. Recent advances in the next-generation sequencing (NGS), the high-throughput, ‘deep’ sequencing technology, have enabled several novel genes to be identified, or found new mutations in known genes. Nevertheless, a substantial fraction of unsolved cases still remain. The primary work in this thesis involves utilizing NGS, particularly whole- exome sequencing, to identify disease-causal mutations in families where at least one parent and affected or unaffected siblings are available.
    [Show full text]
  • Supporting Information
    Supporting Information Poulogiannis et al. 10.1073/pnas.1009941107 SI Materials and Methods Loss of Heterozygosity (LOH) Analysis of PARK2. Seven microsatellite Bioinformatic Analysis of Genome and Transcriptome Data. The markers (D6S1550, D6S253, D6S305, D6S955, D6S980, D6S1599, aCGH package in R was used to identify significant DNA copy and D6S396) were amplified for LOH analysis within the PARK2 number (DCN) changes in our collection of 100 sporadic CRCs locus using primers that were previously described (8). (1) (Gene Expression Omnibus, accession no. GSE12520). The MSP of the PARK2 Promoter. CpG sites within the PARK2 promoter aCGH analysis of cell lines and liver metastases was derived region were detected using the Methprimer software (http://www. from published data (2, 3). Chromosome 6 tiling-path array- urogene.org/methprimer/index.html). Methylation-specificand CGH was used to identify the smallest and most frequently al- control primers were designed using the Primo MSP software tered regions of DNA copy number change on chromosome 6. (http://www.changbioscience.com/primo/primom.html); bisulfite An integrative approach was used to correlate expression pro- modification of genomic DNA was performed as described pre- files with genomic copy number data from a SNP array from the viously (9). All tumor DNA samples from primary CRC tumors same tumors (n = 48) (4) (GSE16125), using Pearson’s corre- (n = 100) and CRC lines (n = 5), as well as those from the leukemia lation coefficient analysis to identify the relationships between cell lines KG-1a (acute myeloid leukemia, AML), U937 (acute DNA copy number changes and gene expression of those genes lymphoblastic leukemia, ALL), and Raji (Burkitt lymphoma, BL) SssI located within the small frequently altered regions of DCN were screened as part of this analysis.
    [Show full text]
  • Analyses of Porcine Public Snps in Coding-Gene Regions by Re-Sequencing and Phenotypic Association Studies
    Mol Biol Rep DOI 10.1007/s11033-010-0496-1 Analyses of porcine public SNPs in coding-gene regions by re-sequencing and phenotypic association studies Xiaoping Li • Sang-Wook Kim • Kyoung-Tag Do • You-Kyoung Ha • Yun-Mi Lee • Suk-Hee Yoon • Hee-Bal Kim • Jong-Joo Kim • Bong-Hwan Choi • Kwan-Suk Kim Received: 22 April 2010 / Accepted: 11 November 2010 Ó Springer Science+Business Media B.V. 2010 Abstract The Porcine SNP database has a huge number SNPs (16.2%) were found across all the five breeds, and of SNPs, but these SNPs are mostly found by computer 199 SNPs (21.7%) were breed specific polymorphisms. data-mining procedures and have not been well character- According to the SNP locations in the gene sequences, ized. We re-sequenced 1,439 porcine public SNPs from these 916 variations were categorized into 802 non-coding four commercial pig breeds and one Korean domestic SNPs (785 in intron, 17 in 30-UTR) and 114 coding SNPs breed (Korean Native pig, KNP) by using two DNA pools (86 synonymous SNPs, 28 non-synonymous SNPs). The from eight unrelated animals in each breed. These SNPs nucleotide substitution analyses for these SNPs revealed were from 419 protein-coding genes covering the 18 that 70.2% were from transitions, 20.0% from transver- autosomes, and the re-sequencing in breeds confirmed 690 sions, and the remaining 5.79% were deletions or inser- public SNPs (47.9%) and 226 novel mutations (173 SNPs tions. Subsequently, we genotyped 261 SNPs from 180 and 53 insertions/deletions).
    [Show full text]
  • 1 Insights Into Transporter Classifications: an Outline Of
    1 1 Insights into Transporter Classifications: an Outline of Transporters as Drug Targets Michael Viereck,1 Anna Gaulton,2 and Daniela Digles1 1University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria 2EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK 1.1 Introduction Classifications are a useful tool to get an overview of a topic. They show instan- ces grouped together that share common properties according to the creator of the classification, and as in the case of hierarchical classifications, they allow to draw conclusions on the relation of different classes. In the case of the identifica- tion of drug targets (including transporters as the main drug target), several pub- lications show classifications as a helpful tool. Imming et al. [1] categorized drugs according to their targets, to get an esti- mate on the number of known drug targets, including channels and transporters. Drugs on the market were connected to a target only if it was described as the main target in the literature. For transport proteins (including uniporters, sym- porters, and antiporters), this identified six different types of transporter groups that are relevant as drug targets. These are the cation-chloride cotransporter + + + + (CCC) family (SLC 12), Na /H antiporters (SLC 9), proton pumps, Na /K ATPases, the eukaryotic (putative) sterol transporter (EST) family, and the neu- + rotransmitter/Na symporter (NSS) family (SLC 6). These families mainly belong to either ATPases or solute carriers (SLC). Whether the EST family is treated as transport protein or not depends on the classification used. Rask-Andersen et al.
    [Show full text]
  • Roles of ATP-Binding Cassette Transporter A7 in Cholesterol Homeostasis and Host Defense System
    274 Journal of Atherosclerosis and Thrombosis Vol.18, No.4 ApoA-I Enhances Phagocytosis by Stabilizing ABCA7 275 Review Roles of ATP-Binding Cassette Transporter A7 in Cholesterol Homeostasis and Host Defense System Nobukiyo Tanaka, Sumiko Abe-Dohmae, Noriyuki Iwamoto, and Shinji Yokoyama Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, Nagoya Japan ATP-binding cassette transporter (ABC) A7 is an ABC family protein that is a so-called full-size ABC transporter, highly homologous to ABCA1, which mediates the biogenesis of high-density lipo- protein (HDL) with cellular lipid and helical apolipoproteins. ABCA7 mediates the formation of HDL when exogenously transfected and expressed; however, endogenous ABCA7 was shown to have no significant impact on the generation of HDL and was found to be associated with phagocytosis regulated by sterol regulatory element binding protein 2. Since phagocytosis is one of the fundamen- tal functions of animal cells as an important responsive reaction to infection, injury and apoptosis, ABCA7 seems to be one of the key molecules linking sterol homeostasis and the host defense system. In this context, HDL apolipoproteins were shown to enhance phagocytosis by stabilizing ABCA7 against calpain-mediated degradation and increasing its activity, shedding light on a new aspect of the regulation of the host-defense system. J Atheroscler Thromb, 2011; 18:274-281. Key words; ABCA7, ApoA-I, HDL, Phagocytosis, ABCA1, Cholesterol brane protein for cholesterol homeostasis, for the
    [Show full text]